Coffee- a sip of thousand chemicals

Cup glass of coffee with smoke and coffee beans on old wooden background

Presenting you an interesting collection of information about one of the favourite beverages among the academicians – coffee.

Most of us will agree that on cold January mornings, a mug of cappuccino with extra sugar is a guiltless morning indulgence. Just one sip and a thousand chemicals swirl in the bloodstream, making the heart race, happily refreshing up our minds and spirits to kick start the day ahead.

But the story of coffee limits itself neither to the Nescafe sachets nor to the rim of the coffee mugs. It is in fact, much deeper and wider than the coffee mugs. Truly, in the modern world, we are so much surrounded by CCDs, Starbucks, and cafes that we take this bitter brew too much for granted. The journey of coffee in our culture certainly deserves a bit of attentive retelling. Because it has a fascinatingly rich history, momentous presence, and a promising future ahead. 

The Origin

Let me begin with how coffee came into human cognition and got rapidly popularized around the globe. The word coffee is derived from the Arabic word “quaweh/quawah[i]” which means to give vigor or strength[ii]. Legend has it that coffee was discovered by an Ethiopian herder, Kaidi around the 9th century AD[iii]. While roaming around the countryside of the Ethiopian kingdom of Kaffa[iv], he observed that his goats turned very agile when they chewed upon the berries of a certain shrub (which we now know as Coffea arabica). Being curious, he took a few of the berries to the nearby mosque to understand the phenomena. Probably, then the imam and his companions brewed the unroasted beans or directly ate them raw. Consequently, they could remain awake throughout the night during their prayers. Later on, the Sufis adopted the practice of drinking coffee for sustaining their fasting rituals.

The Middle-East

In 1000 AD, the Arabs began the first to roast and grind coffee and brewed it just with hot water[v]. They were also the first to build coffee plantations in Yemen around that time. Before the 1600s, the port of Al Mukka was the single center of coffee export and marketing to the rest of the world iii. In the 1600s, a Sufi saint from Chikmaglur, Karnataka called Baba Budan[vi] smuggled out seven coffee seeds and planted them in Chandragiri hills in the westerns ghats of South India. In the early 1700s, the Dutch began to cultivate it in Sri Lanka. At the end of that century, the Dutch, as they spread the plant from Java, Sumatra, Celebes, Bali, and other islands of East Indies eventually took over the monopoly of the coffee trade vi.

In Europe

The lifestyle in Europe visibly changed upon the introduction of coffee. Europeans back in the 17th century had little idea about the concept of germs. But they altogether avoided drinking water. The concept of drinking boiled water was also not in rage in the popular psyche at that time. Instead, they would drink ale or wine even in their breakfast. But alcohol had an intoxicating effect. Since coffee allowed boiled water in its preparation it became safe to drink and acted as a substitute for alcohol. Thus, coffee came to be revered as a sober drink[vii]. In 1668, the colonists in New York replaced beer with coffee as a drink for breakfast i.

Further West

Very soon coffee became an indispensable drink for the intelligentsia for its stimulant effect. Coffee houses began to mushroom around the cities where intellectuals gathered and shared their opinions of their days. In many cases, historical decisions were made inside the coffee houses. One such incident is Paul Revere plotting the American Revolution at the Green Dragon Coffee House in Boston i

In India

In India, coffee proudly graced in the court of Jahangir as depicted by Reverend Edward Terry, an Englishman who visited the Mughal court in 1616 [viii]. But the coffee culture of Mughal India soon collapsed under the rise of the British who were primarily tea drinkers. But in Victorian times, as the demand for coffee rose in upper-class clubs, the British Raj eventually took interest in the commercial production of coffee in India. They established arabica coffee plantations in south India. Coffee percolated in Indian society at large as it came to be served in clubs like Bengal Club in Calcutta 1827, Madras Club in 1832, and Bangalore club in 1863. The first coffee house outlet was established in Church gate street in Bombay in 1936 viii. The coffee house in college street Kolkata was established in April 1876 and has remained a witness to the city’s political and intellectual history.

The Present

The importance of coffee in the modern economy is immense. Coffee brewed from roasted beans is one of the most popular beverages in the world and the second-largest merchandised liquid in the world just after petroleum[ix]. It is grown in more than 70 countries reaching a worldwide production of greater than 10 megatons per year ix. The geographical region from 30 N to 30S latittude is recognized as coffee belt region as it supports the growth of coffee plantations from sea level to 2000 m[x]. At present, Brazil is the largest producer of coffee in the world followed by Vietnam and Colombia[xi].

Diversity of Coffee

There are about 500 species of coffee xi in the world but the coffee we drink comes mainly from Coffea canephora (robusta) and Coffea arabica. The taste of coffee depends upon the species of the plant from which berries are collected and various other factors like processing of the beans, preparing the drink, etc. Coffee can be enjoyed in various styles of brews -Turkish style, French Press, Expresso, Scandinavian boiled coffee, instant, etc. It is also taken in as a concoction with alcohol called liqueur in some countries. Kahlua and Tia Maria to name a few are some of the famous coffee liqueurs[xii].

The Chemistry Behind Coffee

Chemically, coffee is a complex mixture of carbohydrates, lipids, vitamins, antioxidants, polyphenols and alkaloids, and other biologically active compounds[xiii]. According to a study conducted by Nestle, coffee contains four times higher antioxidant concentrations than green tea alone[xiv]. Upon roasting of the coffee beans, around 1000 compounds are generated through chemical reactions like Maillard reaction, carbohydrate caramelization, and pyrolysis of the complex organic compounds[xv]. Analytical techniques such as Chromatography; voltammetry; mass spectrometry; UV spectroscopy, FTIR, ATR, HPLC, paper substrate room temperature phosphorescence, NMR, electrophoresis have revealed that coffee consists of a broad banner of chemical compounds[xvi]. Caffeine, theophylline, and theobromine fall under the category of methylxanthines; diterpenes which include kahweol and cafestol are exclusively present in coffee. Phenolic compounds include some 14 Chlorogenic acids and their derivatives like lactones such as caffeoylquinic acids (CQA) with 3 isomers (3-, 4- and 5-CQA), dicaffeoylquinic acids (diCQA) with 3 isomers (3,4-diCQA; 3,5-diCQA; 4,5-diCQA), feruloylquinic acids (FQA) with 3 isomers (3-, 4- and 5-FQA), p-coumaroylquinic acids (pCoQA) with 3 isomers (3-, 4- and 5- pCoQA) and mixed diesters of caffeoylferuloylquinic acids (CFQA). Apart from them, bioactive phenolics such as isoflavones, lignans, tannins, and anthocyanins are also present in the coffee brew. Micronutrients found in coffee are Mg, K, niacin, nicotinic acid and its precursor trigonelline, vitamin E, etc xvi.

Image 1: Gallery of compounds present in coffee; Credit: Eur Food Res Technol (2015) 240:19–31

The amount of variation of these compounds not only influences the aroma and flavor of the coffee but also helps to distinguish the different species of coffee. For example, green beans of Coffea arabica contain between 0.7 and 1.6 % of caffeine whereas Coffea canephora has 1.5 and 4.0 % xvi. The content of trigonelline in coffee beans of Arabica was slightly higher than in Robusta (1.03 vs. 0.9 %) on the dry weight basis. Coffee beans contain 0.15–0.37 % (Robusta) and 0.27– 0.67 % (Arabica) d.m. of cafestol. In the mature beans, mainly citric and malic acids were found at about 1.5 and 0.4 %, respectively. Among inorganic ions, phosphates dominated. They were found at a concentration of 0.1 %. After the roasting process, concentrations of citric and malic acids slightly decrease. Simultaneously, formic, acetic glycolic and lactic acids considerably increase. However, the phosphates are little affected by the roasting process. Compounds like caffeine and chlorogenic acids which are abundant in green coffee get also get reduced in content during roastingxv. The degradation of trigonelline during the roasting process generates many aromatic compounds in various concentrations that help to differentiate the roasting temperatures between arabica and robusta. Instant coffee contains a 1,000-fold higher level of phytoestrogens than coffee brew.

As far as the aroma and flavor are concerned Warner Gross Group detected some characteristic 22 odorants in coffee through the stable isotope analysis method iii. Some aroma molecules of coffee are 2- furfuryl thiol (coffee-like), 2-ethyl-3,5-dimethylpyrazine (roasty), Furaneol (caramel-like), and 3-methylbutanal (malty), guaiacol (medicinal), β-damascenone (fruity), and 2,3- butanedione (buttery)[xvii]. Additional fact for coffee connoisseurs, you can consult to coffee flavor wheel as reported by Palmiro Patronieri and Franca Rossi in their paper published in 2016[xviii]

Image 2: Coffee Flavour wheel ; Credit: Specialty Coffee Association of America (SCAA) and World Coffee Research (WCR) (©2016)

Have you ever observed that you taste something sweet at the back of your throat when you use perfumes with fruity notes?

Then you probably can understand the term “taste-odor synthesia”. It means smelling induces taste. An interesting study on taste-odor synesthesia was conducted based on espresso coffee brew samples in 2008 where the scientists wanted to know if the reverse happens to be true or not. The authors described how adding creamer and sweet changes the relative volatility of the flavor compounds in coffee and how the perception of the flavor of the brew changed upon the addition of them xvii.

It was found out that upon adding creamer, the content of a molecule called EDM-pyrazine drastically reduced but it did not alter the overall perception of the flavor. Perception-wise, upon adding creamer, the flavor intensity of factors like maltiness, roasty, and caramel did not vary significantly from the pure black brew. On the other hand, upon adding sugar, compounds like Furaneol, furfuryl thiol, and EDM pyrazine concentrations were unaffected.

As mentioned earlier Furaneol gives caramel like flavour to the coffee. They observed that although its concentration did not alter in presence of sugar the intensity of caramel flavour increased considerably. The intensity of malty sensation remained unchanged with and without added sweetener. The roasty and coffee-like ratings both decreased to similar extents in the samples after the addition of sweeteners. The intensity of caramel was considerably increased. They compared the results with two different kinds of sweeteners – sucrose and sucralose, the latter being 700 fold concentrated than the former. The intensity of the flavor profiles changed to similar extents in both cases. Since the added sweeteners were both non-volatile, they concluded that it is a case where taste affected odor perception as people often generally associate the sweet taste with caramel and  barbeque roast. Their work highlighted the fact that the perception of flavor was not directly related to the content of volatile organic compounds in coffee alone but had a complex association with memories associated with enjoying similar kinds of dishes having the same taste.

Image 3: Variation of coffee flavour intensity upon addition of additives; Credit: Chem. Percept. (2008) 1:147–152

Now, each of these chemicals in coffee offers unique benefits to human health. Isoflavones such as daidzein, genistein, or formononetin and lignans such as secoisolariciresinol, matairesinol, pinoresinol, or lariciresinol are used to protect from hypercholesterolemia, carcinogenesis, and osteoporosis. They also are said to relieve menopausal symptoms. An antioxidant named methylpyridinium which is found exclusively in coffee and formed during the roasting process is said to reduce colon cancer xiv. Cafestol and Kahweol present uniquely in coffee are said to increase cholesterol levels in blood serum xiv. Melanoidins are involved in inhibiting proteins called zinc-based metalloproteases which play some crucial role in colon cancer xiv. Theophylline and Theobromine which dilates blood vessels and reduces inflammation in guts[xix]. Palmitates help to reduce free radical content from serum xix. Coffee is also said to drive away suicidal thoughts.

Out of all the chemicals mentioned, Caffeine deserves special attention alone. It is said that Caffeine is to coffee as theobromine is to chocolate. In other words, coffee without caffeine is like a rose without its sweet scent. Still thanks to Ludwig Roselius[xx], one can too enjoy decaffeinated coffee since the 1900s. Decaffeinated coffee contains 5-25mg/L of caffeine whereas caffeinated coffee has 300-1650mg/L of caffeine xiv. On average a single espresso shot contains 58-76 mg of caffeine[xxi].

Biomedical Aspects of Coffee

 In 1820, Pierre Robiquet isolated a compound called caffeine which is the main stimulant in coffee[xxii]. His paper is one of the early reported accounts about the investigation on chemical constituents of coffee. Caffeine (1,3,7 trimethylxanthine) is a purine alkaloid xiv, xxi. Once ingested it gets rapidly absorbed in the stomach and small intestine walls xxi. It generally interacts with adenosine receptors. Adenosine is a neuromodulator that has an inhibitory effect like slowing down the heartbeat, reducing alertness, etc xxi. As Caffeine blocks those receptors it produces a stimulant effect in the body. It increases blood pressure, metabolic rate, diuresis and stimulates the central nervous system xxi. Caffeine also generates heat and promotes weight loss[xxiii]. It has been found that after 16 weeks of continuous caffeine intake, it stimulated the production of catecholamines to increase the oxidation and metabolism of fatty acids xxiii. However, there is a little catch. A study on Korean women of both premenopausal and postmenopausal categories reported that a positive correlation exists between obesity and coffee consumption xxiii. It could be because Koreans generally consume coffee with creamer and sweeteners.  

95% of Caffeine metabolism is carried out by cytochrome P450 isoform named CYP1A2 in the liver xxi. n the 1920s, German scientists discovered that caffeine solutions could open up the bile ducts and stimulate the production of bile in the liver. Thus, it helps to expel the carcinogenic substances from the liver and the colonic wall xix. Thus, the use of coffee as enemas came into the rage. In case you don’t know what enema is let me describe it but you might find it gross. Enema is a fluid that gets injected into the rectum to clear out the bowel and administer drugs or food. Dr. Max Gerson started the use of coffee enemas for his cancer patients in 1930 xix. The story gets even darker when people started overusing it and died owing to electrolyte imbalance. 

A study reported that caffeine shows 50% antimicrobial effect upon a bacteria strain called S. enterica xv. Though Caffeine alone exhibits weak antibacterial activity, it is said to enhance the overall antimicrobial activity of R-dicarbonyl compounds like glyoxal, methylglyoxal, and diacetyl compounds by which are formed during the roasting process of the beans xv. Nowadays, caffeine extracted from coffee silverskin, a seed coat -a main by-product after the roasting process is increasingly used in cosmetics due to its high biological activity and its ability to penetrate through the skin barrier[xxiv]. Amazingly enough, during that research artificial human skin was used as the model for the assay. It is a great optimistic step for people who strongly express dissent against the use of animals during the testing of cosmetic products.

Coffee is also quite a bit like Dr. Jekyll and Mr. Hyde. WHO classifies coffee as a group 2B carcinogenxiv. Coffee is said to aggravate gastric cancer, kidney and bladder cancer. Coffee increases the risk of high blood pressure, stroke, and coronary heart disease though many studies find it to be inconclusive. Some people also experience heightened nervousness, insomnia, nausea, and abdominal pain xxi Excessive coffee intake can increase the risk of osteoporosis especially in elders[xxv]. Coffee also penetrates the placenta and thus might increase the risk of spontaneous abortion and premature birth xxi,[xxvi]. Withdrawal symptoms of coffee include headaches, fatigue, drowsiness, difficulty in concentration, and depressed mood xxi.

Environmental Concerns

Coffee waste management is a colossal problem. The coffee we drink comes from the coffee bean i.e., seed. The bean size on average is 10 mm long and 6mm wide[xxvii]. About 18% of the coffee cherry i.e., the fruits are composed of the green bean[xxviii]. The remaining part of the fruit which is composed of pulp, mucilage, pectin layer, and parchment is inedible and thus goes to waste. There are three types of coffee waste: dry husk, pulp, and spent coffee grounds xxviii. The general way of processing coffee is the wet method which involves a large amount of water to ferment and remove the pulp and mucilage from the coffee beans. In this process, a huge amount of wastewater is generated. Resultant wastewater is rich in organic compounds and has high BOD (9600 mg/L)[xxix]. They also contain caffeine which has adverse environmental effects. Caffeine inhibits seed germination, increases toxicity in insects and certain bacteria xxviii. As this wastewater decomposes it produces a foul smell that persists for a long time. It also causes eutrophication. Let me explain how grand this problem is. A study from Kenya reports that a factory that produces 1ton/d of clean coffee generates wastewater equivalent to domestic sewage of about 2000 people xxix. So, a country that produces over 120000 tons of coffee represents a population equivalent to about 240000000! Apart from the wastewater, a significant amount of solid waste also gets produced which includes dry husks, fermented pulps which are perfect breeding grounds for flies. 

Image 4: The anatomy of a coffee cherry; Credit: Feedipedia

Researchers and engineers have come up with ingenious solutions for this problem. Dry husks are incinerated and provide energy. In 2017, activated carbon from coffee husk was used to remove chromium(V1) from industrial waste water xxiii. It is a serious finding as chromium is carcinogenic. Moist pulps are put in anaerobic digesters from where methane is produced. Even successful attempts have been made to convert pulp into bioethanol. Regarding wastewater, conventional methods like activated sludge, oxidation ditches are used now along with innovative biotechnological applications. Scientists have started employing certain genetically modified bacteria instead fungi to decaffeinate the wastewater before dumping it into mainland water bodies. Earlier for decaffeination, most attempts have been performed with fungi. Penicillium verrucosum, Aspergillus tamari V12A25, and Aspergillus sp. have all been used in solid-state fermentation to decaffeinate coffee husk, coffee pulp, and husk. The resultant decaffeinated coffee waste may serve as animal feed due to its nutrient content. Decaffeinated coffee waste may also be more readily used as potting soil for various ornamentals. Decaffeinated coffee waste may have great potential as a feedstock for biofuels. Coffee waste contains 45-60% (dry weight) carbohydrates, which could be fermented to biofuels, such as ethanol or butanol. However, prevailing levels of caffeine in the waste can be toxic to yeast. Therefore, decaffeination may be an important first step in the utilization of coffee waste as a biofuel’s feedstock. Fermented coffee pulps are used as grounds for growing mushrooms like shitake which are considered seasonal delicacies and hence have high market value[xxx]. Coffee pulp also has cation exchange properties especially in the context of removing cationic dyes from industrial effluents xxx. Coffee silverskin has turned out as an excellent source for soluble dietary fibers and its content is higher than cereals such as oatmeal. Coffee silverskin is now explored to produce prebiotics as it supports the growth of helpful gut bacteria like bifidobacteria[xxxi].

What about the waste materials after preparing the brew?

Spent coffee ground is a residue produced after the coffee brew is made. It has attracted the attention of scientists worldwide. In 2015, a paper reported the application of activated carbon obtained from spent coffee grounds for methane storage[xxxii]. Activated carbon from the spent coffee ground is also used in capacitors for lithium-ion batteries xxxii. Graphene-based quantum dots are synthesized from carbonized spent grounds which can act as effective nano drugs against fighting Parkinson’s disease as they can easily pass through the blood-brain barrier and prevent the formation of abnormal α-synuclein fibrils which are responsible for this neurodegenerative disease[xxxiii]. In 2013, another paper reports the generation of biodiesel from spent coffee grounds upon transesterification process for about 73.4% w/w[xxxiv]. Interestingly, in 2019, a research group has utilized spent coffee ground for the production of humidity sensors as well[xxxv].

Image 4: Graphical abstract from a published paper describing how coffee waste products can be managed; Credit: Haile / Biofuel Research Journal 2 (2014) 65-69

Coffee and Corruption!

Certainly, and sadly, coffee too is not free from the clutches of corruption. The price of coffee depends upon the quality of beans, the time required for cultivation, and the processing cost. For example, Kona coffee beans grown in Kenya are very expensive as they are highly revered for their quality in the coffee industry. Ridiculously, 20 million Kona coffee beans are sold annually where only 2 million pounds are grown in a year. To contain such coffee adulteration and fluctuating market price, a team of scientists in 2002 came up with the idea of chemical profiling of coffee through multi-elemental analysis along with the aid of statistical methods using neural networks. Elemental analysis was already in practice the quality check of potatoes. Earlier, the quality of the coffee was determined based upon analysis of volatile organic compounds that generate the odor profile of the coffee. Such practice was inappropriate for determining provenance as they were subjected to storage conditions and brew techniques. Finally, they found out that elements like Al, Cd, and P turned out to be effective differentiating factors of coffee grown in Central and South America and East Africa thereby helping to curtail down the adulteration of beans x.

The Final Comments

People now recognize coffee as a functional food. It has inspired many chemists to find solutions to fight against diseases and find innovative ways to make a sustainable living. However, climate change is also posing serious threats to coffee growth and hence the rising price of coffee. But that is something we can compromise. After all, coffee is indeed a mesmerizing drink with a versatile range of benefits that have won most of our hearts and it deserves to do so! 

About the author:

Shrestha Chowdhury is currently working as a Senior Research Fellow in the Department of Chemical Sciences at IISER KOLKATA. For her second blog in TQR platform, she has attempted to pen down her thoughts about a drink towards which she was priorly indifferent. Glad to say, she has started to enjoy the beverage after the completion of the project! She also dedicates this article to one of her close friends and avid coffee addict Ms. Sakshi Balasaria.


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[vii] The history of the world in 6 glasses by Tom Standage


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[xi] Eur Food Res Technol (2015) 240:19–31 DOI 10.1007/s00217-014-2356-z

[xii] Chang-Hwan Oh, International Journal of Emerging Trends in Engineering Research, 8(9), September 2020, 4990 – 4994

[xiii] Relationship between Coffee Consumption and Cancer- A Review; B. John Rozar Raj et al /J. Pharm. Sci. & Res. Vol. 8(6), 2016, 424-427

[xiv] Vol 13 May 2012

[xv] Isolation, Identification, and Quantification of Roasted Coffee Antibacterial Compounds; MARIA DAGLIA, † ADELE PAPETTI, † PIETRO GRISOLI, ‡ CAMILLA ACETI, † VALENTINA SPINI, † CESARE DACARRO, ‡ AND GABRIELLA GAZZANI*,†; J. Agric. Food Chem. 2007, 55, 10208–10213

[xvi] Analytical methods applied for the characterization and the determination of bioactive compounds in coffee; Magdalena Jeszka-Skowron · Agnieszka Zgoła-Grzes´kowiak · Tomasz Grzes´kowiak; Eur Food Res Technol (2015) 240:19–31 DOI 10.1007/s00217-014-2356-z

[xvii] Taste–Odor Integration in Espresso Coffee; Ariya Chiralertpong & Terry E. Acree & John Barnard ; Chem. Percept. (2008) 1:147–152 DOI 10.1007/s12078-008-9018-0

[xviii] Challenges in Specialty Coffee Processing and Quality Assurance; Palmiro Poltronieri 1,* and Franca Rossi 2; Challenges 2016, 7, 19; doi:10.3390/challe7020019

[xix] COFFEE: THE ROYAL FLUSH ; Ralph W. Moss, From The Cancer Chronicles #6 and #7


[xxi] Jane V. Higdon & Balz Frei (2006): Coffee and Health: A Review of Recent Human Research, Critical Reviews in Food Science and Nutrition, 46:2, 101-123 To link to this article:

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[xxiii] Nutrients 2017, 9, 1340; doi:10.3390/nu9121340

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[xxv] Korean J Fam Med. 2014;35:1

[xxvi] van der Hoeven T, Browne JL, Uiterwaal CSPM, van der Ent CK, Grobbee DE, Dalmeijer GW (2017) Antenatal coffee and tea consumption and the effect on birth outcome and hypertensive pregnancy disorders. PLoS ONE 12(5): e0177619.


[xxviii] Cent. Eur. J. Chem. • 12(12) • 2014 • 1271-1279 DOI: 10.2478/s11532-014-0550-2

[xxix] COFFEE INDUSTRY WASTES; B. Gathuo*, P. Rantala** and R. Maatta*; War. Sci. Tech. Vol. 24, No. 1, pp. 53-60, 1991.

[xxx] Potential alternative uses of coffee wastes and by-products; Rajkumar Rathinavelu and Giorgio Graziosi; ED 1967/05 17 August 2005 Original: English

[xxxi] Ref 10

[xxxii] Nanotechnology 26 (2015) 385602 (8pp); doi:10.1088/09574484/26/38/385602

[xxxiii] Nanomaterials 2021, 11, 1423. 11061423

[xxxiv] INTERNATIONAL JOURNAL of RENEWABLE ENERGY RESEARCH Mebrahtu Haile et al., Vol.3, No.4, 2013

[xxxv] Sensors 2019, 19, 801; doi:10.3390/s19040801

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